When waves around harbors are computed with Boussinesq models, so-called “sponge layer” is placed along the computational region to absorb reflected waves going out to open sea. The wave absorbing characteristics of the sponge layer for long period waves have not yet been fully clarified. Using two-dimensional numerical wave-tank with a sponge layer just behind the wave generating boundary, regular waves of 20, 60, 100, 200 and 300 sec were generated, and its wave absorbing characteristics were investigated through the wave height of the standing waves generated in the wave tank. It was found that the reflected waves entering from the region to the sponge layer are almost completely absorbed by properly setting the sponge stiffness and the sponge thickness. Further investigation on water surface oscillations near the boundary of the harbor was carried out. It was found that by providing thin sponge layer along the impermeable boundary, abnormal water surface oscillations, which occasionally occur around the boundary corner, can be effectively suppressed.